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SlicerElastix

This extension makes available Elastix medical image registration toolkit (https://elastix.lumc.nl) available in Slicer.

Installation

  • Download and install latest stable release or a recent nightly release of 3D Slicer (https://download.slicer.org).
  • Start 3D Slicer application, open the Extension Manager (menu: View / Extension manager)
  • Install SlicerElastix extension (in Registration category)

Register two volumes

  • Start 3D Slicer
  • Load your volumes (for example: switch to SampleData module and load MRBrainTumor1 and MRBrainTumor2 images)
  • Switch to General registration (Elastix) module (in Registration category)
  • Select Fixed volume (for example: MRBrainTumor1)
  • Select Moving volume (this volume will be resampled to match voxels of the Fixed volume; for example: MRBrainTumor2)
  • Select Preset: generic (all) performs deformable registration; generic rigid (all) performs rigid registration
  • Select "Create new Volume" for Output volume (this will be the resampled moving volume)
  • Select "Create new Transform" if later you want to visualize the displacement field or apply the transform to other nodes (points, surfaces, other volumes)
  • Click Apply button and wait a couple of minutes

Visualize and save results

  • To compare Fixed volume with Output volume (registered moving volume): set Fixed volume as Foreground volume in slice viewers and fade between the Output volume and Foreground volume to see how well they are aligned.
  • To display displacement field: in Transforms module, select the Output transform and in Display section enable visualization in slice and/or 3D views.
  • To apply transforms to other nodes: use Transforms module (or in Data module / Transform hierarchy tab: drag-and-drop nodes under the Output transform).
  • To save Output volume or transform, select menu: File / Save.

Customize registration parameters

  • Click Show database folder in Advanced section, which will open the tolder that contains all registration preset parameter files
  • Edit the parameter set database file (ElastixParameterSetDatabase.xml) to edit or add a new preset (each ParameterSet element defines one preset)
  • To modify parameters of a registration step, edit the corresponding .txt parameter file